"This government is determined to finish the job with a hand of steel against evil," Gloria Arroyo said on Thursday.
She said this after soldiers killed 10 Abu Sayyaf separatists in an hour-long gun battle on the southern island of Jolo.
"The relentless pressure we have applied in the field is taking its toll and we will keep it up until all terrorists and their clandestine cells are accounted for," Arroyo said.
The statement comes a day after the military said it killed Abu Sulaiman, one of Abu Sayyaf's top five leaders.
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Last week government troops killed Binang Sali, considered a spiritual leader of the group accused of kidnapping and beheading tourists, and carrying out deadly bomb attacks.
Lieutenant-Colonel Bartolome Bacarro, a military spokesman, said on Thursday: "Right now, they are suffering from a leadership vacuum and they are now disorganised. We will keep up the tempo."
Last week, the Philippines signed a convention on counter-terrorism with its South-East Asian neighbours during the Association of South-East Asian Nations summit.
Arroyo said the agreement would "tighten the dragnet and stop the movement of terrorists, their finances and their deadly material across the seas and borders".
Abu Sayyaf has only about 400 core members, but it has been held responsible for the Philippines' worst terrorist attack, the bombing of a ferry near Manila Bay in 2004 that killed at least 100 people.
The group is said to have links with Jemaah Islamiyah, which is believed to be fighting for a pan-Asian Islamic state, and also with al-Qaeda.
Al Jazeera's Veronica Pedrosa says now that Abu Sulaiman been killed, the Philippine military is warning that there may be revenge attacks.
The group originally broke off from larger separatist armies, fighting for an independent Muslim homeland in the mostly Christian Philippines.
The Abu Sayyaf became less interested in the cause than in lucrative kidnapping operations, Pedrosa said.
They are also believed to have strong links with al-Qaeda linked Jemaah Islamiyah.
Abu Sulaiman is only one face, however, in the gallery of the Philippines' most wanted.
The top leader of the group is Khadaffy Janjalani.
The Philippine military think they may have killed him in September, but results of DNA tests haven't been announced yet, Pedrosa said.